Blender Textures to Unity
I'm not quite sure if this will work but it's worth a shot...
In Unity, delete all the materials except the one you want to use with the texture atlas. Make sure the texture for that material is actually your texture atlas. You will then notice that the mesh render's on most of the objects in Unity will look like the following:

All you should have to do is drag the same material that your texture atlas is on, onto that slot. Make sure to do that with all of your objects selected so you can do that all at once.